I'm afraid your query is beyond me but wanted to reply in the hope others may take the time to contribute.
Are you saying there is an external IBM Domino server in one environment and in your environment you have neither an IBM Domino server or an IBM Notes client installed? Further that you're trying to execute code on the Linux Server which will then interact with the Domino Server in the other environment? On my Windows IBM Notes client the Notes.jar file is installed to C:\Program Files (x86)\IBM\Lotus\Notes\jvm\lib\ext
Sadly I know very little of Linux or JRE but I can't help feeling your goal is somewhat ambitious!
Always good to hear people are still trying clever things with Domino.
Good luck.